Dear Justin:<br><br>Thanks so much for your effort and information. Perhaps I did not set the proper value for vdw_switch. I will try some value. I really appreciate your nice help!<br><br><div class="gmail_quote">On Mon, May 18, 2009 at 5:24 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Perhaps I can contribute something else that might be a bit more useful. It just occurred to me that if you are only changing the vdwtype parameter, then you are not correctly implementing the shift function. See here for proper use of a shift potential:<br>
<br>
<a href="http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#vdw" target="_blank">http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#vdw</a><br>
<br>
Take note of the necessary changes to vdw_shift, and potentially rlist. A few quick tests of the shift function indicate the following:<br>
<br>
Case 1. Plain cutoff's at 1.2 nm<br>
Density: 988 kg/m^3<br>
<br>
Case 2. Shift potential (no other changes, i.e. rvdw_switch = 0, rvdw = 1.2)<br>
Density: 962 kg/m^3<br>
<br>
Case 3. More appropriate shift potential (rvdw_switch = 1.0, rvdw = 1.2)<br>
Density: 983 kg/m^3<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Yanmei Song wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Justin:<br>
<br>
Yes and I tried dispersion correction and it gives a larger density than I expected. The density of the polymer by vdwtype=shift is more close to the experimental value. Then your suggestion would be to choose the vdwtype=cut-off under this condition even if it result in larger density? Thank you so much!<br>
<br>
</blockquote>
<br>
No. My suggestion is to do your homework, as Mark originally said, and as I echoed in my last mail. Read about the water model, its expected performance under different simulation parameters, and evaluate what you want to do once you have done this background work. If you have done a thorough literature review, there is no one else that can make a choice for you; decide how to handle your system based on what you read.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Yanmei Song wrote:<br>
<br>
Dear Justin:<br>
<br>
Yes. Before I do the water+polymer, I did both the bulk systems<br>
separately. The density of TIP5P I mentioned earlier is the<br>
results for pure water bulk system. My concern is that if it is<br>
reasonable that the property of the system changes with<br>
different mdp conditions? Since when I did the bulk water and<br>
bulk polymer system, I found the densities change with different<br>
cutoff and vdwtype conditions. Is this a artifact? Or the larger<br>
cutoff, the more accurate result we can get?<br>
<br>
<br>
Every parameter you specify will affect the results you see. I<br>
agree with Mark - look up the original reference for TIP5P and see<br>
what parameters are recommended. Also read the subsequent<br>
literature that has used TIP5P to see what modifications<br>
(electrostatic treatment, vdW treatment, etc) are appropriate or<br>
even more accurate.<br>
<br>
Also realize that using vdwtype = shift may not be the best<br>
solution. I only suggested as a guess for something to try back<br>
when you were getting bizarre results with your polymer. Have you<br>
ever tried dispersion correction when using vdwtype = cutoff? I<br>
routinely use such a setup and have never seen any really bizarre<br>
behavior.<br>
<br>
-Justin<br>
<br>
On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
Yanmei Song wrote:<br>
<br>
Dear Mark:<br>
<br>
Thanks for your answer. I have to use the same mdp file<br>
for both<br>
water and another polymer molecules in my system, right?<br>
Then<br>
if the shift function works well for the polymer, I can<br>
not get<br>
the best result for TIP5P? The density of TIP5P is different<br>
from the literature value of 982. Thanks!<br>
<br>
<br>
So your system is water + polymer? In that case, you have an<br>
added<br>
variable - the interaction between the water and your<br>
polymer. What<br>
you should probably be more concerned with the what the bulk<br>
density<br>
of the whole system is. I have found that analyzing densities of<br>
portions of mixed systems does not give an accurate result.<br>
<br>
-Justin<br>
<br>
<br>
On Mon, May 18, 2009 at 3:33 PM, Mark Abraham<br>
<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>>> wrote:<br>
<br>
Yanmei Song wrote:<br>
<br>
Dear All:<br>
<br>
I found when I changed the vdwtype from cut-off to<br>
shift, the<br>
density of the system decrease significantly.All<br>
the other<br>
setting in the mdp file remain unchanged. For<br>
example the<br>
density of TIP5P water drops to 962. Does it mean<br>
I can<br>
not use<br>
the shift for vdwtype?<br>
<br>
<br>
Maybe not. Check out the paper in which TIP5P was<br>
parameterized. The<br>
greater the extent to which your .mdp conditions<br>
differ from<br>
those<br>
conditions, the greater the likelihood that the<br>
parameterization is<br>
no longer valid.<br>
<br>
Mark<br>
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Virginia Tech<br>
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Department of Chemical Engineering<br>
Arizona State University<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
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Department of Chemical Engineering<br>
Arizona State University<br>
</blockquote>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>